Workflow

This pipeline is for the analysis of a Lemur TB sample sequenced on Nanopore. The repository for the pipeline can be found at <https://github.com/mbhall88/LemurPaper>

Click the nodes to obtain details about each step.

AMR Prediction

Quality Control

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
File Code
config.yaml 
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fast5_dir:    "fast5/"
model_config: "dna_r9.4.1_450bps_hac_prom.cfg"  # the basecalling model config
decontam_db:  "/hps/nobackup/research/zi/projects/tech_wars/data/QC/decontam_db/"
containers:
  guppy:  "library://mbhall88/default/guppy-gpu:3.4.5"
  conda:  "docker://continuumio/miniconda3:4.7.12"
  pycoqc: "docker://quay.io/biocontainers/pycoqc:2.5.0.23--py_0"
  krona:                "docker://quay.io/biocontainers/krona:2.7--pl526_2"
  mykrobe: "docker://quay.io/biocontainers/mykrobe:0.8.2--py36h1c69254_1"
envs:
  aln_tools:            "envs/aln_tools.yaml"
  filter_reads:         "envs/filter_reads.yaml"
  rg:                   "envs/rg.yaml"
  generate_krona_input: "envs/generate_krona_input.yaml"
scripts:
  filter_reads:         "scripts/filter_reads.py"
  generate_krona_input: "scripts/generate_krona_input.py"
captions:
  pycoqc:  "report/pycoqc.rst"
  krona:   "report/krona.rst"
  mykrobe: "report/mykrobe.rst"

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